April 17

Outlining and Lysin Analyzing (4/15/19)

Rationale:

Outline an abstract about the individual research project and use bioinformatic tools to analyze different lysins that infect Arthrobacter.

Procedure:

  1. Outlined an abstract about individual research project.
  2. Used tools such as PhagesDB, NCBIp BLAST, and TMHMM to analyze AL, AM, and AN cluster phages’s lysins and holins.

Results:

The following image shows the outline created.

The following images show the chart created to organize data collected from search.

(Clusters AL (Shrooms) –– AN (Muttlie)-21ktwwj)

Conclusion:

After looking through phages from Cluster AL (Shrooms) to Cluster AN (Muttlie) it was found that generally AL cluster phages had a lysin A with a PGRP superfamily CDD with a holin. AM clusters generally had an endolysin around gene 5 with a Peptidase_M23 superfamily CDD with holin. AN cluster phages generally either had two lysin A with one lysin A with a Peptidase_M23 superfamily CDD at gene 16 and the other lysin A with a PGRP superfamily CDD and a holin around gene 18. The other commonly found pattern followed in AN cluster phages was an endolysin and a holin around gene 18. Despite having two different trends all AN cluster lysin genes had the same Pham numbers. Only AM cluster phages had the “HLH” catalytic region.

Future Work:

Continue analyzing different phages lysins and holins.

Category: Kathryn Adkins | LEAVE A COMMENT
April 17

DNA Day 23

17 April 2019 ✷ More Independent Research

Rationale: The trends in the percent GC of the genes were analyzed and justification was sought out.

Procedure

  • Gene 97 was blasted again to see what bacteria CDD matched it with
  • Gene 97 hit with stapholococcus virus psi12
  • articles found by the group noted that GC content was lower in Staphylococcus
  • an abstract was written
  • gene 62 was looked at, but it hit with a high GC bacteria
  • an abstract was completed

Results

the abstract

Conclusion

Having a gene that is shared with phages of other clusters and is similar to a virus with a lower CG supports the idea that horizontal gene transfer could be responsible for the low GC content associated with AM phages.

Future plans

Find more data and work on presentation

Category: Lily Goodman | LEAVE A COMMENT
April 17

DNA Day 22

15 April 2019 ✷ More Independent Research

Rationale: The trends in the percent GC of the genes were analyzed via statistical methods and further research plans were decided upon to answer the research question.

Procedure

  • Justification for why AM phages had such a low GC content when arthrobacter has a typically high GC content was researched on databases.
  • An abstract was drafted
  • it was decided that the remainder of the research would come from literature and databases including NCBI and PubMed were used to locate more information on GC and arthrobacter.

Results

A research outline was created

Conclusion

TGC is related to bond strength because of the three bonds between C and G. This allows DNA to be more resistant to high temperature. Horizontal gene transfer is responsible for a lot of the variation in GC content of bacteria and the phages that infect them.

Future plans

Find more data!

Category: Lily Goodman | LEAVE A COMMENT
April 17

4.15.19 Work on Independent Projects

4.15.19 Work on Independent Projects

Rationale: More work needed to be done to correctly determine the identity and function of the sequence of interest. Therefore, time today was spent using online tools to determine a potential function for the sequence.

Procedure:

  • Found a tool that was able to identify transposable elements (IS Finder)
  • Read primary literature to obtain any other ideas surrounding sequences similar to the one found and being investigated
  • Looked for other tools that could be used to help predict the function of the sequence

Results:

  • The transposable elements finder showed no direct hits to any organism in the database
  • Primary literature search did not reveal any new information, but pointed to new tools that needed to be tested out – tools did not have a very good success rate

Conclusions

  • Since the sequence is officially not a transposable element, the new struggle is finding something that the sequence could be. We have disproved the notion that the sequence is other likely components, and therefore we need to seek a new function or path that can hopefully contextualize the sequence and give direction to a potential function.

Next Steps: Finding a new function that could be applied to the sequence of interest

Category: Henry Burns | LEAVE A COMMENT
April 17

April 17 2019 Independent Research Project and Abstract

Purpose: The purpose of this lab is to continue to work on the independent research project, as well as write an abstract for the final project.

Tools/Procedures:

Tools:

  • DNA Master
  • PhagesDB
  • NCBI BLAST

Procedures:

  1. Research was done to determine if there was any evidence of horizontal gene transfer in NapoleonB. It was found that gene 62 showed high similarity with Streptomyces bacteria and that gene 97 showed similarity with a Streptococcus virus.
  2. More research was done to show that %GC and genome length of phage are inversely related.
  3. An abstract was written for the final project, including information collected from this lab and previous labs.

Results:
The research done in this lab helped to provide evidence for horizontal gene transfer and its role in the %GC of NapoleonB. NapoleonB’s gene 97 matched with a Streptococcus virus. Streptococcus is a low GC bacteria in the phylum Firmicutes. The correlation with gene 97 provides evidence that horizontal gene transfer could be a reason the phage has a %GC much lower than its host, arthrobacter. It was also found that %GC and genome length are inversely related. As NapoleonB and most AM phages have longer genomes, around 150,000 base pairs, this is another possible explanation for the lower GC content.

Conclusion:
In conclusion, this lab helped to provide possible evidence for why AM phages have a lower %GC than their arthrobacter host.

Future Work:
Future work will include continuing research on GC content of phage and host. It will also include beginning to create a final presentation for the project and drawing conclusions from the data and sources collected.

Category: Lucy Potts | LEAVE A COMMENT
April 17

Presentation Outline and Continued Research 4/15/19

Presentation Outline and Continued Research 4/15/19

Rationale

The rationale behind today in lab was to create a project outline to help guide the rest of our research and to help us begin to prepare for our final presentations. In addition, when we were done with our presentation outline, we continued working on sequencing and protein folding in order to collect the necessary data.

Tools/Procedure

  1. Presentation outline was submitted
  2. MEME Motif was used to find repeating motifs in the TMPs of selected proteins from each usable cluster

Results

The results above were generated using the MEME software to find motifs. The logo above represents a motif that was found in all selected TMPs except one, suggesting an area of conservation. When all of the TMPs have been folded, we will see if we can use the protein folding information to support this motif being conserved structurally as well.

Conclusion

While there is not enough data to make extensive conclusions yet, our data so far suggests that while there are significant differences among TMPs outside of their clusters, there do appear to be at least some similarities, which answers our guiding question.

Future Plans

In the future, we will continue to look for similarities and difference in the amino acid while continuing our folding of proteins to try to figure out if there are key conserved regions in TMPs. I will compare all 43 selected TMPs to ensure that the above-identified motif is as universal as it appears.

Category: Uncategorized | LEAVE A COMMENT
April 17

Discovering supercluster 34265 4/17/19

Rationale: I’m continuing the process described in the previous post to try to discover new superclusters.

Tools: PhagesDB, Phamerator

Procedure:

1. Looked through DNA primase phams and looked through phams within the AK cluster.

2. Noticed a plateau in the pham cluster members similar to when looking at the pham cluster members of NapoleonB.

3. Recorded my findings.

Results: The clusters that contain  a lot of similar synteny and similar phams:

 

  • AK
  • EA7
  • EJ

Conclusions and Future Work: Now that I’ve found a couple instances of what could be described as superclusters I need to find a numerical way or visual way to display my findings of these common syntenys and genes.

 

Category: Sriram Avirneni | LEAVE A COMMENT
April 17

Independent Research Outline 4/15

Rationale: Create an outline for CURES presentation and finish hard data for minor tail proteins.

Procedure: Word document was made and outline was made. Reviewed primary literature to help construct both an abstract and introduction. Google sheets, DNA Master, and PhagesDB were used to help analyze the starts of the Arthrobacter phage minor tail proteins. The last few minor tail protein starts preferences were entered.

Results: Outline and the end list of the minor tail proteins (613 minor tail proteins).

Future work: Start structure analysis and to examine start the start sites of all tail proteins. See correlation between the starts and length. and see why there was a reverse minor tail protein.

Conclusions: Finished the hard data and analysis of starts will be done 4/17. The overall process of collecting data took longer than expected. Figure out another way to gather data that would take less time i.e. Phamerator or code.

Category: Michael Lum | LEAVE A COMMENT
April 15

April 15 2019 Independent Research Project Presentation Outline

Purpose: The purpose of this lab was to begin outlining the presentation for the research project and the final presentation in May.

Tools/Procedures:

Tools:

  • Google Drive
  • PubMed/NCBI
  • PhagesDB

Procedures:

  1. The data from the last lab was analyzed and discussed to determine the next step in the project.
  2. It was decided that a literature search would need to be done to learn more about the %GC in host and phage genome, and the relationship between their GC content.
  3. Articles were found discussing the phage and hos GC content.
  4. A project outline was created for the presentation.
  5. An abstract was started, and a background information section was also begun. The results are not finished, but the current findings were compiled. The conclusion was also begun.

Results:
An outline for the project was created, with elements such as the abstract, background information, and conclusion. The articles found showed that in most bacteriophage there is a correlation between their %GC and that of their host. It was also found that the longer the phage genome was, the lower the %GC. It was also found that the average %GC of Arthrobacter sp. ATCC 21022 is 63.41%.

Conclusions:
In conclusion, it was determined that more literature needed to be read to try and determine the reason that the AM phage %GC is so much lower than that of its host. An outline was created for the final presentation.

Future Work:
Future work will include learning more about the GC correlation of phage and their host species through literature searches. Also, more work will need to be done for the final presentation.

Category: Lucy Potts | LEAVE A COMMENT
April 15

Discovering Supercluster 45806 4/15/19

Rationale: After talking to Dr. Pope at the phage emporium I decided the best move is to look at modules containing genes that originate in bacteria to find more superclusters. By finding more superclusters I can compare against the one I’ve already found to make the claim that these are a thing.

Tools: PhagesDB, Phamerator

Procedure:

1. I started by searching through phams in phagesDB that are called as cas4 exonucleases.

2. I looked at the phamerator maps of multiple clusters containing a cas4 exonuclease and tried to find patterns in the gene synteny.

3. Discovered another instance of what might be a supercluster that contained a module of DNA primase followed by a DNA polymerase.

Results:

Clusters found to contain similar synteny and the 45806 primase module:

  • AZ
  • BB
  • BB1
  • BB2
  • BJ
  • BL
  • EB
  • EH

Conclusions and Future Work: This method of discovering new superclusters seems to work quite well I’m going to continue looking for more superclusters so I can compare them against each other.

 

Category: Sriram Avirneni | LEAVE A COMMENT